Contacts of the strand formed by residues 247 - 251 (chain C) in PDB entry 3HYW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 247 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 3.6 25.4 - - + -
132C THR* 3.9 9.0 - - + -
135C LYS* 3.9 37.5 - - + -
136C LEU* 3.5 35.7 - - + -
139C LEU* 4.2 17.0 - - + -
145C PRO 3.2 3.9 + - - +
146C VAL* 3.3 31.9 - - + -
147C VAL 3.0 23.4 + - - -
163C PHE* 3.9 19.1 - + - -
167C LEU* 4.3 3.1 - - + -
245C ALA* 4.3 0.3 - - - +
246C LYS* 1.3 79.1 - - + +
248C THR* 1.3 74.8 + - - +
249C MET* 4.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN 4.0 4.1 + - - +
120C SER* 2.7 34.5 + - - -
121C THR* 2.6 37.3 + - - +
147C VAL* 3.1 11.2 - - + +
226C ILE* 3.6 10.9 - - + +
227C GLU 5.4 2.0 - - - +
231C VAL* 3.6 19.3 - - + -
245C ALA* 3.6 24.9 - - + -
246C LYS 5.5 0.4 - - - -
247C PHE* 1.3 86.2 - - - +
249C MET* 1.3 55.2 + - - +
250C PHE* 4.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 3.3 26.2 - - - +
122C SER* 3.8 12.3 - - - -
123C ILE* 4.0 22.9 - - + -
132C THR* 4.6 0.2 - - + -
147C VAL 3.1 5.9 + - - -
148C ILE* 3.2 19.6 - - + +
149C GLY 3.1 21.0 + - - -
160C ALA* 4.2 2.7 - - + -
163C PHE* 3.6 47.3 - - + -
247C PHE* 4.1 2.6 - - + -
248C THR* 1.3 74.1 - - - +
250C PHE* 1.3 66.3 + - - +
251C MET* 3.1 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN* 3.8 20.8 + - - +
120C SER* 3.5 6.3 + - - +
121C THR 3.1 15.4 + - - +
122C SER* 3.9 7.6 - - - -
147C VAL* 3.7 40.6 - - + -
148C ILE 4.0 1.1 - - - -
149C GLY* 3.3 35.2 - - - -
150C ALA* 3.4 10.8 - - - -
151C ILE* 4.2 7.4 - - + -
185C ILE* 3.9 5.6 - - + -
223C VAL* 3.6 23.8 - - + -
226C ILE* 3.6 23.1 - - + -
231C VAL* 4.0 25.1 - - + -
248C THR* 4.1 3.1 - - - -
249C MET* 1.3 83.2 - - - +
251C MET* 1.3 61.3 + - - +
252C PRO* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN* 3.6 3.7 + - - -
122C SER* 6.5 0.2 - - - -
123C ILE* 3.7 20.6 - - + +
124C CYS* 4.3 17.9 - - - -
149C GLY 2.9 19.2 + - - +
150C ALA* 4.3 3.4 - - + -
151C ILE* 3.4 14.6 + - - +
154C VAL* 3.4 25.7 - - + +
156C CSS 3.7 24.7 - - - +
157C PHE* 5.2 0.2 - - - -
159C PRO* 3.8 9.2 - - + -
160C ALA* 3.5 27.6 - - + +
249C MET* 3.1 36.3 - - + -
250C PHE* 1.3 72.8 - - - +
252C PRO* 1.3 69.5 - - + +
700C H2S 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il